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Dr. Alexander Shakeel Bates

I am a neuroscientist and programmer on open-source projects. I work on insect brains. I am interested in how neurons wire together, and how they work together to build complex, innate behaviours. D.O.B. 23/09/1993.

total_cites h_index i10_index
1990 17 17

Professional Research

Postdoctoral Fellow in Neurobiology

Harvard Medical School

Boston, US

present - 01/10/2020

  • Member of the laboratory of Prof. Rachel Wilson
  • Working on navigational circuitry, using calcium imaging, neurophysiology and behavioural studies involving virtual reality with D. melanogaster

Visiting Scientist

Dept. Zoology, University of Cambridge

remote

present - 01/10/2020

Grants

Sir Henry Wellcome Fellowship

Wellcome Trust & University of Oxford

UK

01/06/2025 - 01/06/2022

  • 30,000 GBP towards my current research
  • Collaboration between groups of Rachel Wilson, Wei Lee, Scott Waddell and Shaul Druckmann

EMBO fellow

European Molecular Biology Organization

Europe

01/06/2022 - 01/04/2021

Life Science Research Foundation Fellowship

Life Science Research Foundation

US

2021

  • Did not pursue

Human Frontiers Fellowship

International Human Frontier Science Program

International

2021

  • Did not pursue

Herchel Smith PhD Scholarship

Herchel Smith Foundation

Cambridge, UK

30/09/2019 - 01/08/2015

Boehringer Ingelheim PhD Scholarship

Boehringer Ingelheim Foundation

European

01/08/2018 - 01/08/2016

Skills

  • R
  • python
  • MATLAB
  • github
  • git
  • markdown
  • Illustrator
  • InDesign
  • communication
  • text editing
  • journalistic writing
  • creative writing
  • open access



Peer Reviews

journal reviews
PLoS Computational Biology 3
eLife 3
Nature Communications 1



Referees

Education

Neuroscience PhD

MRC LMB, University of Cambridge

Cambridge, UK

30/09/2020 - 01/09/2015

Neuroscience BSc

University College London

London, UK

01/07/2015 - 01/09/2012

A levels

Woodbridge High School

London, UK

01/09/2012 - 01/09/2010

  • 6 A*s at A-level, comprising: Physics, Chemistry, Mathematics, English Literature, Philosophy and Russian, and in a history related EPQ (level 3) project

GCSEs

Woodbridge High School

London, UK

31/08/2010 - 01/09/2008

  • 13 A*s: English Literature, English Language, Mathematics, Statistics, Core Science, Additional Science, History, Philosophy, Geography, French, Italian, Russian and Expressive Arts. Jack Petchey Achievement Award

Reviews

title author journal year cites
1 Systems neuroscience: Auditory processing at synaptic resolution AS Bates, G Jefferis Current Biology 2022 1
6 Neuronal cell types in the fly: single-cell anatomy meets single-cell genomics AS Bates, J Janssens, GS Jefferis, S Aerts Current opinion in neurobiology 2019 59

Papers

This table shows all of my work, searchable on pubmed. Author list displays firt six. My name in bold, underlining indicates first (co)authorship. Get in contact for information on recents projects.

Most of my work has first been published on bioRxiv

Much of my work comes with open source R code

title author journal year cites
2 Information flow, cell types and stereotypy in a full olfactory connectome P Schlegel, AS Bates, T Stürner, SR Jagannathan, N Drummond, J Hsu, … Elife 2021 89
3 Complete connectomic reconstruction of olfactory projection neurons in the fly brain AS Bates, P Schlegel, RJV Roberts, N Drummond, IFM Tamimi, … Current Biology 2020 140
4 Neurotransmitter Classification from Electron Microscopy Images at Synaptic Sites in Drosophila Melanogaster N Eckstein, AS Bates, A Champion, M Du, Y Yin, P Schlegel, AKY Lu, … bioRxiv 2020 65
5 The natverse, a versatile toolbox for combining and analysing neuroanatomical data AS Bates, JD Manton, SR Jagannathan, M Costa, P Schlegel, T Rohlfing, … Elife 2020 135
7 Functional and anatomical specificity in a higher olfactory centre S Frechter, AS Bates, S Tootoonian, MJ Dolan, J Manton, AR Jamasb, … Elife 2019 84
8 Whole-brain annotation and multi-connectome cell typing quantifies circuit stereotypy in Drosophila P Schlegel, Y Yin, AS Bates, S Dorkenwald, K Eichler, P Brooks, DS Han, … bioRxiv 2023 19
9 Discriminative attribution from paired images N Eckstein, H Bukhari, AS Bates, GSXE Jefferis, J Funke European Conference on Computer Vision 2022 4
10 BAcTrace, a tool for retrograde tracing of neuronal circuits in Drosophila S Cachero, M Gkantia, AS Bates, S Frechter, L Blackie, A McCarthy, … Nature methods 2020 25
11 Neurogenetic dissection of the Drosophila lateral horn reveals major outputs, diverse behavioural functions, and interactions with the mushroom body MJ Dolan, S Frechter, AS Bates, C Dan, P Huoviala, RJ Roberts, … Elife 2019 124
12 Communication from learned to innate olfactory processing centers is required for memory retrieval in Drosophila MJ Dolan, G Belliart-Guérin, AS Bates, S Frechter, A Lampin-Saint-Amaux, … Neuron 2018 93
13 Automated reconstruction of a serial-section EM Drosophila brain with flood-filling networks and local realignment PH Li, LF Lindsey, M Januszewski, Z Zheng, AS Bates, I Taisz, M Tyka, … bioRxiv 2019 85
14 Network Statistics of the Whole-Brain Connectome of Drosophila A Lin, R Yang, S Dorkenwald, A Matsliah, AR Sterling, P Schlegel, S Yu, … bioRxiv 2023 0
15 Neuronal wiring diagram of an adult brain S Dorkenwald, A Matsliah, AR Sterling, P Schlegel, SC Yu, CE McKellar, … bioRxiv 2023 26
16 A leaky integrate-and-fire computational model based on the connectome of the entire adult Drosophila brain reveals insights into sensorimotor processing PK Shiu, GR Sterne, N Spiller, R Franconville, A Sandoval, J Zhou, … bioRxiv 2023 4
17 The connectome of the adult Drosophila mushroom body provides insights into function F Li, JW Lindsey, EC Marin, N Otto, M Dreher, G Dempsey, I Stark, … Elife 2020 221
18 A connectome and analysis of the adult Drosophila central brain LK Scheffer, CS Xu, M Januszewski, Z Lu, S Takemura, KJ Hayworth, … Elife 2020 648
19 Connectomics analysis reveals first-, second-, and third-order thermosensory and hygrosensory neurons in the adult Drosophila brain EC Marin, L Büld, M Theiss, T Sarkissian, RJV Roberts, R Turnbull, … Current Biology 2020 75
20 Input connectivity reveals additional heterogeneity of dopaminergic reinforcement in Drosophila N Otto, MW Pleijzier, IC Morgan, AJ Edmondson-Stait, KJ Heinz, I Stark, … Current Biology 2020 50
21 Neural circuit basis of aversive odour processing in Drosophila from sensory input to descending output P Huoviala, MJ Dolan, FM Love, P Myers, S Frechter, S Namiki, … bioRxiv 2018 40
22 Combinatorial encoding of odors in the mosquito antennal lobe P Singh, S Goyal, S Gupta, S Garg, A Tiwari, V Rajput, AS Bates, … Nature Communications 2023 3

Selected Talks

ECRO meeting

European Chemoreception Research Organization

Trieste, Italy

2019

Boehringer Ingelheim Meeting

Boehringer Ingelheim Fonds

Hirschegg, Austria

2018

MPI Connectomics meeting

Max Planck Institute

Berlin, Germany

2017

ECRO meeting

European Chemoreception Research Organization

Cambridge, UK

2017

Boehringer Ingelheim Meeting

Boehringer Ingelheim Fonds

Hirschegg, Austria

2017

Brains and Roses

Schaeffer and Datta group organised

Montserrat, Catalonia

2016

Selected Posters

HHMI Investigators’ Meeting

HHMI HQ

Chevy Chase

2023

UK Neural Computation

University of Nottingham

Nottingham, UK

2019

Boehringer Ingelheim Fonds communication workshop

Boehringer Ingelheim Foundation

Mainz, Germany

2017

Maggot Meeting

Janelia Research Campus

Ashburn, US

2016

High-resolution circuit reconstruction meeting

Janelia Research Campus

Ashburn, US

2016

LMB GSA Symposium

MRC LMB, University of Cambridge

Cambridge, UK

2016

Leadership

President of BlueSci

University College London

London, UK

01/10/2019 - 01/01/2016

  • Lead BlueSci, the University of Cambridge’s science media society, throguh 15 issues of the magazine

Mentored summer student

MRC LMB, University of Cambridge

Cambridge, UK

2018

Mentored undergraduate student

Dept. Zoology, University of Cambridge

Cambridge, UK

01/05/2018 - 01/09/2017

  • Student won best thesis in year award and two authorships

Mentored summer student

MRC LMB, University of Cambridge

Cambridge, UK

2017

LMB graduate symposium lead organiser

MRC LMB, University of Cambridge

Cambridge, UK

2017

LMB graduate symposium organiser

MRC LMB, University of Cambridge

Cambridge, UK

2016

President of the UCLU Writer’s Society

University College London

London, UK

01/10/2015 - 01/10/2014

Science Editor, Pi Magazine

University College London

London, UK

01/10/2015 - 01/10/2014

UCL iGEM 2014 Advisor

University College London

London, UK

2014

  • Project planning, oversight, team slection and management
  • Gold medallist

Other

Visiting Scholar

Janelia Research Campus

Ashburn, US

2019

Paris Spring School in Neuroscience Techniques

Paris Descartes University

Paris, France

2018

  • A course in Optical Imaging and Electrophysiological Recording in Neuroscience

Visiting Scholar

Janelia Research Campus

Ashburn, US

2016

University of Queensland Winter Scholarship

University of Queensland

Brisbane, Australia

2015

Amgen Scholarship

Dept. Zoology, University of Cambridge

Cambridge, UK

2014

UCL iGEM 2013 team member

University College London

London, UK

2013

  • Team member, cloning, cell culture, project planning
  • Gold medallist

Summer student in the biomolecular modelling laboratory

Cancer Research UK, London Research Institute

London, UK

2013

Disclaimer

Made with the R package pagedown and datadrivencv.

Code available on GitHub.

Last updated on 2023-11-27.